April 20, 2016

Introduction

Plant root and nodule metagenomes

Endophytic metagenome (NL)

Weller, D.M. et.al (2002). Microbial Populations Responsible for Specific Soil Suppressiveness to Plant Pathogens. Annual Review of Phytopathology 40, 309–348.

Nodule metagenome (Brazil)

Márcio Leite

Sequencing details

Feature Nodule Endo
Platform MiSeq MiSeq + HiSeq
Read length 300 300
Samples 18 10
Raw 8.32 Gbp 191.6 Gbp
QC 4.16 Gbp 47.2 Gbp
Gbp sample 0.23 4.72

Diversity plots

Assembly

Analysis pipeline

Assembly results

Feature Nodule Endo
assembler megahit SPAdes
% mapped 99.65
properly paired 78.16
N50 10,631 1,652
Average cov 1.6
# essential genes 5,769
Nodes 133,461
Edges 152,761

Annotation

pipeline

pictures victorc

Victor Carrión

Binning

Sangwan, N., Xia, F., and Gilbert, J.A. (2016). Recovering complete and draft population genomes from metagenome datasets. Microbiome 4, 8.

Mad Albertsen

GC vs coverage

16S

Colored bins

Tetra nucleotide

Tetra colored

Completeness/contamination Checkm

Bin Id Marker Lineage Completeness Contamination
bin.3 f__Paenibacillaceae 99.85 0.02
bin.8 o__Actinomycetales 99.81 0
bin.7 f__Moraxellaceae 99.51 0.82
bin.9 f__Moraxellaceae 99.45 0.14
bin.4 g__Burkholderia 98.46 0.57
bin.10 o__Bacillales 97.80 1.34

Endosphere binning

Conclusion

  • increasing diversity nodule, endo, rhizo
  • extract full length 16S
  • difference 16S/ metagenome
  • automated/manual binning
  • 16S in bins

Acknowledgements

  • Vittorio Tracanna
  • Noriko Cassman
  • Victor Carrion
  • Marcio Leite
  • Juan Perez
  • Eiko Kuramae
  • Jos Raaijmakers

Average Genome Size

Gene length

Rhizo vs Endo

  • plot diversity

Image test

Image test2

Slide with centered image and citation

[@lindquist_wager_2015]